Protein Primary Structure

Question 1

Describe the structure of an amino acid.

Answer 1

A central (alpha) carbon atom covalently linked to:

• amino group (-NH2)
• carboxyl group (-COOH)
• hydrogen atom (-H)
• distinctive R group

Question 2

What is the acid-base behaviour of aa determined by?

Answer 2

R group

Question 3

Which parts of amino acids can ionise?

Answer 3

The carboxyl group and the amino group:

• ionisation of amino group from -NH2 to -NH3 = base (proton acceptor)
• ionisation of carboxyl group from -COOH to -COO- = acid (proton donor)

Question 4

Why is the acid-base behaviour of aa not determined by ionisation of carboxyl and amino groups? What is it determined by?

Answer 4

• Because amino acids joined together by peptide bonds - form aa residues. Only 1 -NH3+ at N-terminal end, and 1 -COO- at C-terminal end.
• Chemical properties of R group.

Question 5

Which properties of aa R groups are used to classify aa?

Answer 5

1. Charge
2. H bonding ability
3. Acidic vs basic

Question 6

What are the 2 main groups of amino acids?

Answer 6

1. Non-polar; hydrophobic

2. Polar; hydrophilic

Question 7

What is the difference between alkyl/aliphatic and aromatic aa?

Answer 7

• Aliphatic: have C and N in side chain

- Aromatic: benzene ring

Question 8

What is the difference between neutral, acidic and basic aa?

Answer 8

• Neutral: contain oxygen or sulphur atom - attract electrons to that end of the side chain - localised negative and positive ends to side chain.
• Acidic: have -COO- as part of side chain (lost proton)
• Basic: have -NH+ as part of side chain (gained proton)

Question 9

What does the pK value of side chains tell us?

Answer 9

How likely it is to ionise.

• strong base - high pK
• strong acid - low pK

Question 10

How does the solution pH determine R group protonation?

Answer 10

• If solution pH < pK - R group is protonated (base)
• If solution pH > pK - R group is deprotonated (acid)
• If solution pH = pK - Neutral aa

Question 11

How can the ratio of protonated/deprotonated aa side chains be calculated?

Answer 11

• Henderson-Hasselback equation

- pH = pKa + log([A-]/[HA])

Question 12

What is the isoelectric point (pI) of a protein?

Answer 12

PH at which there it has no overall net charge.

Question 13

What is the pI of basic and acidic proteins and what does this mean in terms of their protonation?

Answer 13

• Basic protein (pI > 7): contain many positively charged (basic) aa. Protein is protonated.
• Acidic protein (pI < 7): contain many negatively charged (acidic) aa. Protein is deprotonated.

Question 14

How are 2 aa linked together?

Answer 14

• peptide bonds

- by hydrolysis

Question 15

What are the properties of peptide bonds?

Answer 15

1. Planar: C alpha, C, O, N and H all lie in the same plane.
2. Rigid: undergo resonance.
3. Trans conformation: C alpha on opposite sides of peptide bond due to steric clashes.

Question 16

What does resonance mean?

Answer 16

Movement of electrons from C=O to C-N gives partial C=N characteristics: shorter and less flexible - unable to rotate - contributes to polarity.

Question 17

What are the bonds on either side of the peptide bond called and what is special about them?

Answer 17

• Psi (C alpha - C), Phi (C alpha - N)

- Are free to rotate - angles of bonds determines conformation of peptide backbone and the ‘fold’ of the protein.

Question 18

What are conjugated proteins?

Answer 18

• Contain covalently linked chemical components in addition to aa.
• E.g. Lipoproteins linked to lipids, haemoproteins linked to haem.